As mads said make sure you use whatever gain/offset for your flats as you do for imaging. It's not AS important with flats as it is with darks and bias but it can make a difference how the data is scaled.
As far as the vignetting that can vary for many different things. My guess would be that the camera is not exactly centered or there is some tilt to the CCD relative to the objective. You can try rotating your camera 180 degrees and see if the pattern moves or if it stays in the same place to figure out what may be causing it. But overall I wouldn't worry too much about it, provided the flats do their job correctly.
Min and Max exposure values are just used as a range to find your "good" value. Since you have an idea about what your exposures are (1 and 3 seconds) you can probably set this to a min of 1 and a max of 5. Then run the wizard and see what exposure values SGP comes up for your filters. Also for binned images you may need to decrease your lightbox brightness even more if possible.
Thanks,
Jared